Package

Get linelist

Extract variables of potential interest

## # A tibble: 26,756 x 6
##    country city       province date_confirmati… travel_history_lo… import_status
##    <chr>   <chr>      <chr>    <chr>            <chr>              <chr>        
##  1 China   Chaohu Ci… Anhui    22.01.2020       "Wuhan"            imported     
##  2 China   Baohe Dis… Anhui    23.01.2020       "Luzhou Hunan, vi… imported     
##  3 China   High-Tech… Anhui    23.01.2020       "Yinzhou Hunan, v… imported     
##  4 China   High-Tech… Anhui    23.01.2020       ""                 local        
##  5 China   Feidong C… Anhui    23.01.2020       "Wuhan"            imported     
##  6 China   Lu'an City Anhui    24.01.2020       ""                 local        
##  7 China   Fuyang Ci… Anhui    22.01.2020       "Wuhan"            imported     
##  8 China   Huaibei C… Anhui    25.01.2020       "Wuhan"            imported     
##  9 China   Huainan C… Anhui    26.01.2020       "Wuhan"            imported     
## 10 China   Hefei City Anhui    23.01.2020       "Wuhan"            imported     
## # … with 26,746 more rows

Estimate fraction that are imported

Country Cases Fraction imported (linelist only) Fraction imported (WHO sit reps)
Vietnam 16 0.69 0.69
Australia 27 0.87 0.48
Kuwait 56 1.00 0.46
Malaysia 24 0.65 0.46
Bahrain 47 1.00 0.43
Thailand 42 0.35 0.33
United Arab Emirates 21 0.35 0.33
Singapore 106 0.34 0.29
United States 62 0.88 0.24
Japan 254 0.07 0.21
France 100 0.42 0.08
Germany 129 0.15 0.02
Italy 1689 0.02 0.01
South Korea 4212 0.02 0.00
Iran 978 0.00 0.00

Plot cases over time

## Warning: Removed 9 rows containing missing values (position_stack).

## Saving 7 x 5 in image
## Warning: Removed 9 rows containing missing values (position_stack).

Get interventions

## Warning: Missing column names filled in: 'X8' [8]
## Parsed with column specification:
## cols(
##   date_intervention = col_character(),
##   intervention = col_character(),
##   social_distancing = col_character(),
##   country = col_character(),
##   notes = col_character(),
##   ref1 = col_character(),
##   ref2 = col_character(),
##   X8 = col_character()
## )
Intervention Countries that have implemented
Health screening 5
School closure 5
Remote working 4
Travel advisory 4
Government on alert 3
Quarantine 3
Travel restriction 3
Isolation 2
Lockdown 2
Mandatory quarantine 2
Mass gathering advisory 2
Mass gathering cancellation 2
School closure (not related to outbreak) 2
Social event cancellation 2
Suspending flights 2
Travel ban 2
University closure 2
Work closure (not related to outbreak) 2
[Extension] school and work closure 1
Border checks 1
Border control 1
Communciation distancing 1
Communication distancing 1
Communication general 1
Contact tracing 1
Containment to mitigation 1
Decontamination 1
Enhanced care 1
Entry ban 1
Government announcement 1
Healthcare restrictions 1
Mass gathering ban 1
Medical surveillance 1
Prevention measures school 1
Public information 1
Raise awareness flights 1
Raise awareness healthcare staff 1
Raise awareness public 1
Reduced shop hours 1
Resumption public services 1
School restictions 1
School restrictions 1
Social distancing misc 1
Strengthening primary care response 1
Supply 1
Surveillance 1
Travel advice 1
Intervention Countries that have implemented
School closure 5
Remote working 4
Quarantine 3
Isolation 2
Lockdown 2
Mandatory quarantine 2
Mass gathering advisory 2
Mass gathering cancellation 2
School closure (not related to outbreak) 2
Social event cancellation 2
University closure 2
Work closure (not related to outbreak) 2
[Extension] school and work closure 1
Communciation distancing 1
Communication distancing 1
Contact tracing 1
Healthcare restrictions 1
Mass gathering ban 1
Prevention measures school 1
Reduced shop hours 1
School restictions 1
School restrictions 1
Social distancing misc 1
Travel advice 1
Travel restriction 1
Intervention Countries that have implemented
Health screening 5
Travel advisory 4
Government on alert 3
Travel restriction 3
Suspending flights 2
Travel ban 2
Border checks 1
Border control 1
Communication general 1
Containment to mitigation 1
Decontamination 1
Enhanced care 1
Entry ban 1
Government announcement 1
Medical surveillance 1
Public information 1
Raise awareness flights 1
Raise awareness healthcare staff 1
Raise awareness public 1
Resumption public services 1
Strengthening primary care response 1
Supply 1
Surveillance 1
Travel advice 1
## Warning: Column `country` joining factor and character vector, coercing into
## character vector
## Warning: Removed 9 rows containing missing values (position_stack).

## Saving 7 x 5 in image
## Warning: Removed 9 rows containing missing values (position_stack).
## Warning: Column `country` joining factor and character vector, coercing into
## character vector
## Warning: Removed 9 rows containing missing values (position_stack).

## Saving 7 x 5 in image
## Warning: Removed 9 rows containing missing values (position_stack).